[Bioc-devel] affycoretools in devel failed to install
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Jul 29 16:04:49 CEST 2014
----- Original Message -----
> From: "Vojtech Kulvait" <kulvait at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Tuesday, July 29, 2014 4:40:36 AM
> Subject: Re: [Bioc-devel] affycoretools in devel failed to install
>
> Looks like I was right :)
>
>
> 2014-07-29 13:15 GMT+02:00 Martin Morgan <mtmorgan at fhcrc.org>:
>
> > Looks like Dan corrected symbols2indices then Jim made an
> > additional change
> >
> > ------------------------------------------------------------------------
> > r91908 | jmacdon | 2014-06-26 13:16:03 -0700 (Thu, 26 Jun 2014) | 1
> > line
> >
> > Converted to use roxygen2, so all Rd files changed. Also
> > generalized
> > vennSelect2 so it will work with non-Affy data. Added functions to
> > create
> > tables from GO analyses using ReportingTools.
> > ------------------------------------------------------------------------
> > r91900 | d.tenenbaum | 2014-06-26 10:47:24 -0700 (Thu, 26 Jun 2014)
> > | 3
> > lines
> >
> > replace symbols2indices throughout with ids2indices as limma
> > has renamed this function.
> >
> >
> > ... but Jim bumped the version in the wrong direction so Dan's
> > commit
> > never made it to the build system, and the 'latest' version is the
> > version
> > before Dan's.
> >
> > $ svn diff -c91908 DESCRIPTION
> > Index: DESCRIPTION
> > ===================================================================
> > --- DESCRIPTION (revision 91907)
> > +++ DESCRIPTION (revision 91908)
> > @@ -2,7 +2,7 @@
> > Date: 2008-12-15
> > Title: Functions useful for those doing repetitive analyses
> > with Affymetrix GeneChips.
> > -Version: 1.37.2
> > +Version: 1.35.10
> >
> >
> >
I've bumped it to 1.37.3, so these changes should go through.
Thanks,
Dan
> > On 07/29/2014 03:35 AM, Vojtech Kulvait wrote:
> >
> >> This do not help either:
> >>
> >> BiocInstaller::biocLite("limma", type="source")
> >>>
> >> BioC_mirror: http://bioconductor.org
> >> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> >> 3.1.1.
> >> Installing package(s) 'limma'
> >> trying URL '
> >> http://bioconductor.org/packages/3.0/bioc/src/contrib/
> >> limma_3.21.10.tar.gz'
> >> Content type 'application/x-gzip' length 1215791 bytes (1.2 Mb)
> >> opened URL
> >> ==================================================
> >> downloaded 1.2 Mb
> >>
> >> * installing *source* package ‘limma’ ...
> >>
> >> ** libs
> >> gcc -std=gnu99 -I/usr/local/lib/R-3.1.1/include -DNDEBUG
> >> -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o
> >> gcc -std=gnu99 -I/usr/local/lib/R-3.1.1/include -DNDEBUG
> >> -I/usr/local/include -fpic -g -O2 -c weighted_lowess.c -o
> >> weighted_lowess.o
> >> gcc -std=gnu99 -shared -L/usr/local/lib -o limma.so normexp.o
> >> weighted_lowess.o -L/usr/local/lib/R-3.1.1/lib -lR
> >> installing to /usr/local/lib/R-3.1.1/library/limma/libs
> >> ** R
> >> ** inst
> >> ** preparing package for lazy loading
> >> ** help
> >> *** installing help indices
> >> ** building package indices
> >> ** installing vignettes
> >> ** testing if installed package can be loaded
> >> * DONE (limma)
> >>
> >> The downloaded source packages are in
> >> ‘/tmp/RtmpjACGfx/downloaded_packages’
> >>
> >> Updating HTML index of packages in '.Library'
> >> Making 'packages.html' ... done
> >>
> >>> BiocInstaller::biocLite("affycoretools")
> >>>
> >> BioC_mirror: http://bioconductor.org
> >> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> >> 3.1.1.
> >> Installing package(s) 'affycoretools'
> >> trying URL '
> >> http://bioconductor.org/packages/3.0/bioc/src/contrib/
> >> affycoretools_1.37.1.tar.gz
> >> '
> >> Content type 'application/x-gzip' length 6909574 bytes (6.6 Mb)
> >> opened URL
> >> ==================================================
> >> downloaded 6.6 Mb
> >>
> >> * installing *source* package ‘affycoretools’ ...
> >> ** R
> >> ** inst
> >> ** preparing package for lazy loading
> >> Error : object ‘symbols2indices’ is not exported by
> >> 'namespace:limma'
> >> ERROR: lazy loading failed for package ‘affycoretools’
> >> * removing ‘/usr/local/lib/R-3.1.1/library/affycoretools’
> >>
> >
> > I don't think the complaint is about affycoretools
> >
> >>
> >> The downloaded source packages are in
> >> ‘/tmp/RtmpjACGfx/downloaded_packages’
> >>
> >> Updating HTML index of packages in '.Library'
> >> Making 'packages.html' ... done
> >> Warning message:
> >> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> >> installation of package ‘affycoretools’ had non-zero exit
> >> status
> >>
> >>
> >>
> >>
> >> 2014-07-29 12:32 GMT+02:00 Vojtech Kulvait <kulvait at gmail.com>:
> >>
> >> Hi,
> >>> thank you for your replies. I am sending full output of my R
> >>> session
> >>> started few minutes ago.
> >>> The problem is still remaining.
> >>> Best,
> >>> Vojtech.
> >>>
> >>> R version 3.1.1 (2014-07-10) -- "Sock it to Me"
> >>> Copyright (C) 2014 The R Foundation for Statistical Computing
> >>> Platform: x86_64-unknown-linux-gnu (64-bit)
> >>>
> >>> R is free software and comes with ABSOLUTELY NO WARRANTY.
> >>> You are welcome to redistribute it under certain conditions.
> >>> Type 'license()' or 'licence()' for distribution details.
> >>>
> >>> Natural language support but running in an English locale
> >>>
> >>> R is a collaborative project with many contributors.
> >>> Type 'contributors()' for more information and
> >>> 'citation()' on how to cite R or R packages in publications.
> >>>
> >>> Type 'demo()' for some demos, 'help()' for on-line help, or
> >>> 'help.start()' for an HTML browser interface to help.
> >>> Type 'q()' to quit R.
> >>>
> >>> library(BiocInstaller)
> >>>>
> >>> Bioconductor version 3.0 (BiocInstaller 1.15.5), ?biocLite for
> >>> help
> >>>
> >>>> BiocInstaller::biocValid()
> >>>>
> >>> [1] TRUE
> >>>
> >>>> BiocInstaller::biocLite()
> >>>>
> >>> BioC_mirror: http://bioconductor.org
> >>> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> >>> 3.1.1.
> >>>
> >>>> BiocInstaller::biocLite("affycoretools")
> >>>>
> >>> BioC_mirror: http://bioconductor.org
> >>> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> >>> 3.1.1.
> >>> Installing package(s) 'affycoretools'
> >>> trying URL '
> >>> http://bioconductor.org/packages/3.0/bioc/src/contrib/
> >>> affycoretools_1.37.1.tar.gz
> >>> '
> >>> Content type 'application/x-gzip' length 6909574 bytes (6.6 Mb)
> >>> opened URL
> >>> ==================================================
> >>> downloaded 6.6 Mb
> >>>
> >>> * installing *source* package ‘affycoretools’ ...
> >>>
> >>> ** R
> >>> ** inst
> >>> ** preparing package for lazy loading
> >>> Error : object ‘symbols2indices’ is not exported by
> >>> 'namespace:limma'
> >>> ERROR: lazy loading failed for package ‘affycoretools’
> >>> * removing ‘/usr/local/lib/R-3.1.1/library/affycoretools’
> >>>
> >>>
> >>> The downloaded source packages are in
> >>> ‘/tmp/RtmpjACGfx/downloaded_packages’
> >>>
> >>> Updating HTML index of packages in '.Library'
> >>> Making 'packages.html' ... done
> >>> Warning message:
> >>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> >>> installation of package ‘affycoretools’ had non-zero exit
> >>> status
> >>>
> >>> sessionInfo()
> >>>>
> >>> R version 3.1.1 (2014-07-10)
> >>> Platform: x86_64-unknown-linux-gnu (64-bit)
> >>>
> >>> locale:
> >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> >>> [9] LC_ADDRESS=C LC_TELEPHONE=C
> >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>>
> >>> attached base packages:
> >>> [1] stats graphics grDevices utils datasets methods
> >>> base
> >>>
> >>> other attached packages:
> >>> [1] BiocInstaller_1.15.5
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] tools_3.1.1
> >>>
> >>>>
> >>>>
> >>>
> >>>
> >>> 2014-07-25 17:28 GMT+02:00 Martin Morgan <mtmorgan at fhcrc.org>:
> >>>
> >>> On 07/25/2014 04:32 AM, Vojtech Kulvait wrote:
> >>>
> >>>>
> >>>> Hello,
> >>>>> when I try to install affycoretools in devel i get an error:
> >>>>>
> >>>>> * installing *source* package ‘affycoretools’ ...
> >>>>>
> >>>>>
> >>>>> ** R
> >>>>> ** inst
> >>>>> ** preparing package for lazy loading
> >>>>> Error : object ‘symbols2indices’ is not exported
> >>>>> by
> >>>>> 'namespace:limma'
> >>>>> ERROR: lazy loading failed for package
> >>>>> ‘affycoretools’
> >>>>>
> >>>>>
> >>>>>
> >>>>> I think I have up to date instalation of all packages.
> >>>>>
> >>>>>
> >>>> Hi Vojtech -- just to add to the advice, you can use
> >>>>
> >>>> BiocInstaller::biocValid()
> >>>>
> >>>> to check your installation,
> >>>>
> >>>> BiocInstaller::biocLite()
> >>>>
> >>>> to update your current packages.
> >>>>
> >>>> Martin
> >>>>
> >>>>
> >>>> Vojtech.
> >>>>
> >>>>>
> >>>>> [[alternative HTML version deleted]]
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioc-devel at r-project.org mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>
> >>>>>
> >>>>>
> >>>> --
> >>>> Computational Biology / Fred Hutchinson Cancer Research Center
> >>>> 1100 Fairview Ave. N.
> >>>> PO Box 19024 Seattle, WA 98109
> >>>>
> >>>> Location: Arnold Building M1 B861
> >>>> Phone: (206) 667-2793
> >>>>
> >>>>
> >>>
> >>>
> >> [[alternative HTML version deleted]]
> >>
> >>
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> >
> > --
> > Computational Biology / Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N.
> > PO Box 19024 Seattle, WA 98109
> >
> > Location: Arnold Building M1 B861
> > Phone: (206) 667-2793
> >
>
> [[alternative HTML version deleted]]
>
>
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